GATK 2.3 was released on December 17, 2012. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
In the new release for the HaplotypeCaller function does downsampling do anything?
Can we still use --enable_experimental_downsampling?
What is your recommendation.
You no longer need to use `--enable_experimental_downsampling` for anything; the experimental downsampling is now the regular downsampling (see Version history/Version highlights for details) and is used by default by all tools that downsample reads.